E v o l D i r

136 EvolDir December 1, 2012
Final reminder
UC Davis
WORKSHOP IN APPLIED PHYLOGENETICS
at Bodega Marine Laboratory, Bodega Bay, California
March 2V9, 2013
Sponsored by the University of California, Davis and
Bodega Marine Laboratory (additional financial support
provided by the University of Rochester)
http://bodegaphylo.wikispot.org/Front Page Introduction
Phylogenetic methods have revolutionized
modern systematics and become indispensable tools
in evolution, ecology and comparative biology, playing
an increasingly important role in analyses of biological
data at levels of organization ranging from molecules
to ecological communities. The estimation of phylogenetic
trees is now a formalized statistical problem with
general agreement on the central issues and questions.
A nearly standard set of topics is now taught as part of
the curriculum at many colleges and universities. On
the other hand, application of phylogenetic methods to
novel problems outside systematics is an area of special
excitement, innovation, and controversy, and perspectives
vary widely.
This Spring, for the fourteenth consecutive year, we will
teach a workshop for graduate students interested in
applying phylogenetic methods to diverse topics in biology.
The one-week course is an intensive exploration
of problems to which modern phylogenetic approaches
are being applied and the most current statistical tools
and approaches that are used to solve those problems.
We cover a range of topics in ecology, phylogenomics,
functional morphology, macroevolution, speciation, and
character evolution. The course starts with recent advances
in phylogenetic methodology, and then focuses
on methods and tools that can be brought to bear on
these “applied” issues in the context of a given phylogeny.
The course will be held at the Bodega Marine Laboratory
on the Northern California coast, which has on-site
housing. Our newly increased bandwidth and access
to computing clusters allows us to utilize computerintensive
approaches even in a one-week course. The
course format will involve equal parts of lecture, discussion,
and hands-on software training. One afternoon
during the week will be left free for field trips to local
natural areas.
Topics Covered * Estimating, evaluating and interpreting
phylogenetic trees * Recent advances in Bayesian
and Maximum-likelihood estimation of phylogeny * Estimation
of species trees, gene-tree/species-tree con-
flicts * Divergence-time estimation from sequence data:
relaxed clocks, fossil calibration * Analysis of character
evolution: maximum likelihood and Bayesian approaches,
ancestral-state estimation, rates of trait evolution
* Analysis of morphological form, function of
complex character systems * Inference of diversification
rates: detecting rate shifts, testing key innovation
hypotheses * Model specification issues: model selection,
adequacy and uncertainty * Diagnosing MCMC
performance
Instructors for the 2013 workshop * Carl Boettiger *
Gideon Bradburd * Jeremy Brown * Jonathan Eisen
* Rich Glor * Tracy Heath * Mark Holder * John
Huelsenbeck * Luke Mahler * Brian Moore * Samantha
Price * Bruce Rannala * Bob Thomson * Peter Wainwright
Prerequisites Available housing limits course enrollment
to ~30 students. Preference is given to doctoral
candidates who are in the early to middle stages of their
thesis research, and who have completed sufficient prerequisites
(through previous coursework or research experience)
to provide some familiarity with phylogenetic
methods. Unfortunately, because of limits on class size,
postdocs and faculty are discouraged from applying.
Admission and Fees Students will be admitted based on
academic qualifications and appropriateness of research
interests. The course fee is $650. This includes room
and board at BML for duration of the course (arriving
March 2, leaving March 9) and transportation from
Davis to
Application Deadline Applications are due by November
16, 2012. Please send a completed application form
and one letter of recommendation from your major advisor.
Applications should be sent via email as PDFs to
gbradburd@ucdavis.edu. Students will be notified via
e-mail by December 1, 2013 of acceptance.
Application Forms and Information Visit the
Bodega website to for additional information
and to download an application form: http://bodegaphylo.wikispot.org/2013
Workshop Send all
application materials to:
Gideon Bradburd Department of Evolution and Ecology
5343 Storer Hall University of California Davis
Davis, CA 95616 email: gbradburd@ucdavis.edu
“Brian R. Moore”